Journal of Computer-Aided Molecular Design

, Volume 27, Issue 8, pp 655–664 | Cite as

Automated molecule editing in molecular design

  • Peter W. Kenny
  • Carlos A. Montanari
  • Igor M. Prokopczyk
  • Fernanda A. Sala
  • Geraldo Rodrigues Sartori


The ability to modify chemical structures in an automated and controlled manner is useful in molecular design. This Perspective introduces the MUDO molecule editor and shows how automated molecule editing can be used to standardize structures, enumerate tautomeric and ionization states, identify matched molecular pairs. Unlike its predecessor Leatherface, MUDO can also process 3D structures and this capability can be used to link non-covalently docked ligands to proteins.


Ionization Matched molecular pair Molecule editor SMIRKS Structure standardization Tautomer 



We are grateful to the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; Grant Numbers #2011/01893-3 and #2011/20572-3)) and the Conselho Nacional de Pesquisa (CNPq) for financial support. We thank OpenEye for an academic software license and the two anomymous reviewers for their helpful and constructive comments.

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Peter W. Kenny
    • 1
  • Carlos A. Montanari
    • 1
  • Igor M. Prokopczyk
    • 1
  • Fernanda A. Sala
    • 1
  • Geraldo Rodrigues Sartori
    • 1
  1. 1.Grupo de Estudos em Química Medicinal (NEQUIMED), Instituto de Química de São CarlosUniversidade de São PauloSão CarlosBrazil

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